Merge branch 'develop' into displacements2

Author: kavanase

docs/Dev_ToDo.md

@@ -85,6 +85,7 @@
 - Should flick through other defect codes (see
   https://shakenbreak.readthedocs.io/en/latest/Code_Compatibility.html, also `AiiDA-defects`) and see if
   there's any useful functionality we want to add!
+- Add short example notebook showing how to generate a defect PES for carrier capture or NEB calculations (don't use `IBRION = 2` for NEB).
 
 ## SK To-Do for next update:
 - `doped` repo/docs cleanup `TODO`s above

docs/Tips.rst

@@ -453,6 +453,13 @@ etc.).
     defect supercell, directly from just the relaxed structures, regardless of whether these defects were
     generated/parsed with ``doped``.
 
+.. note::
+
+    Wyckoff letters for lattice sites can depend on the ordering of elements in the conventional standard
+    structure, for which doped uses the ``spglib`` convention (e.g. in the ``DefectsGenerator`` info
+    output).
+
+
 Serialization & Data Provenance (``JSON``/``csv``)
 --------------------------------------------------
 To aid calculation reproducibility, data provenance and easy sharing/comparison of pre- and post-processing

doped/analysis.py

@@ -118,7 +118,7 @@ def check_and_set_defect_entry_name(
 ) -> None:
     """
     Check that ``possible_defect_name`` is a recognised format by doped (i.e.
-    in the format "{defect_name}_{optional_site_info}_{charge_state}").
+    in the format ``"{defect_name}_{optional_site_info}_{charge_state}"``).
 
     If the DefectEntry.name attribute is not defined or does not end with the
     charge state, then the entry will be renamed with the doped default name

doped/chemical_potentials.py

@@ -1124,6 +1124,9 @@ def __init__(
         ``DefectEntry.charge_state_guessing_log`` attributes. See docs for examples of
         modifying the generated charge states.
 
+        Note that Wyckoff letters can depend on the ordering of elements in the conventional
+        standard structure, for which doped uses the ``spglib`` convention.
+
         Args:
             structure (Structure):
                 Structure of the host material (as a pymatgen Structure object).
@@ -1836,8 +1839,6 @@ def _defect_generator_info(self):
         info_string += (
             "The number in the Wyckoff label is the site multiplicity/degeneracy of that defect in the "
             f"conventional ('conv.') unit cell, which comprises {fu} formula unit(s) of {formula}.\n"
-            "Note that Wyckoff letters can depend on the ordering of elements in the conventional "
-            "standard structure, for which doped uses the spglib convention."
         )
 
         return info_string
@@ -2172,6 +2173,10 @@ def __repr__(self):
         """
         Returns a string representation of the DefectsGenerator object, and
         prints the DefectsGenerator info.
+
+        Note that Wyckoff letters can depend on the ordering of elements in
+        the conventional standard structure, for which doped uses the ``spglib``
+        convention.
         """
         return (
             self.__str__()

doped/generation.py

@@ -217,7 +217,7 @@ def raw_energy_from_chempots(composition: Union[str, dict, Composition], chempot
     raw_energies_dict = dict(next(iter(chempots["limits"].values())))
 
     if any(el.symbol not in raw_energies_dict for el in composition.elements):
-        raise ValueError(
+        warnings.warn(
             f"The chemical potentials dictionary (with elements {list(raw_energies_dict.keys())} does not "
             f"contain all the elements in the host composition "
             f"({[el.symbol for el in composition.elements]})!"

doped/py.typed

@@ -398,9 +398,9 @@ def get_wyckoff(frac_coords, struct, symm_ops: Optional[list] = None, equiv_site
     symm_dataset, unique_sites = _get_symm_dataset_of_struc_with_all_equiv_sites(
         frac_coords, struct, symm_ops, symprec=symprec
     )
-    conv_cell_factor = len(symm_dataset["std_positions"]) / len(symm_dataset["wyckoffs"])
+    conv_cell_factor = len(symm_dataset.std_positions) / len(symm_dataset.wyckoffs)
     multiplicity = int(conv_cell_factor * len(unique_sites))
-    wyckoff_label = f"{multiplicity}{symm_dataset['wyckoffs'][-1]}"
+    wyckoff_label = f"{multiplicity}{symm_dataset.wyckoffs[-1]}"
 
     return (wyckoff_label, unique_sites) if equiv_sites else wyckoff_label
 
@@ -1126,7 +1126,7 @@ def point_symmetry_from_defect(defect, symm_ops=None, symprec=0.01):
     symm_dataset, _unique_sites = _get_symm_dataset_of_struc_with_all_equiv_sites(
         defect.site.frac_coords, defect.structure, symm_ops=symm_ops, symprec=symprec
     )
-    spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["site_symmetry_symbols"][-1])
+    spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
     if spglib_point_group_symbol is not None:
         return spglib_point_group_symbol
 
@@ -1240,7 +1240,7 @@ def point_symmetry_from_defect_entry(
         # then easy, can just be taken from symmetry dataset of defect structure
         symm_dataset = _get_sga(defect_entry.defect.structure, symprec=symprec).get_symmetry_dataset()
         return schoenflies_from_hermann(
-            symm_dataset["site_symmetry_symbols"][defect_entry.defect.defect_site_index]
+            symm_dataset.site_symmetry_symbols[defect_entry.defect.defect_site_index]
         )
 
     supercell = _get_defect_supercell(defect_entry) if relaxed else _get_bulk_supercell(defect_entry)
@@ -1344,15 +1344,15 @@ def point_symmetry_from_defect_entry(
             # This issue is avoided for relaxed defect supercells as we take the symm_ops of our reduced
             # symmetry cell rather than that of the bulk (so no chance of spurious symmetry upgrade from
             # equivalent sites), and hence the max point symmetry is the point symmetry of the defect
-            spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["site_symmetry_symbols"][-1])
+            spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
 
             # Note that, if the supercell is non-periodicity-breaking, then the site symmetry can be simply
             # determined using the point group of the unrelaxed defect structure:
             # unrelaxed_defect_supercell = defect_entry.calculation_metadata.get(
             #     "unrelaxed_defect_structure", defect_supercell
             # )
             # return schoenflies_from_hermann(
-            #     _get_sga(unrelaxed_defect_supercell, symprec).get_symmetry_dataset()["pointgroup"],
+            #     _get_sga(unrelaxed_defect_supercell, symprec).get_symmetry_dataset().pointgroup,
             # )
             # But current approach works for all cases with unrelaxed defect structures
 
@@ -1361,15 +1361,15 @@ def point_symmetry_from_defect_entry(
             # the defect (e.g. for split-interstitials, split-vacancies, swapped vacancies etc),
             # so use 'pointgroup' output (in this case the reduced symmetry avoids the symmetry-upgrade
             # possibility with the equivalent sites, as when relaxed=False)
-            spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["pointgroup"])
+            spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.pointgroup)
 
             # This also works (at least for non-periodicity-breaking supercells) for relaxed defects in
             # most cases, but is slightly less robust (more sensitive to ``symprec`` choice) than the
             # approach above:
             # schoenflies_from_hermann(
             #     _get_sga(
             #         defect_supercell, symprec=symprec
-            #     ).get_symmetry_dataset()["pointgroup"]
+            #     ).get_symmetry_dataset().pointgroup
             # )
 
     if spglib_point_group_symbol is not None:
@@ -1416,7 +1416,7 @@ def _check_relaxed_defect_symmetry_determination(
 
     if unrelaxed_defect_structure is not None:
         unrelaxed_spglib_point_group_symbol = schoenflies_from_hermann(
-            _get_sga(unrelaxed_defect_structure, symprec=symprec).get_symmetry_dataset()["pointgroup"],
+            _get_sga(unrelaxed_defect_structure, symprec=symprec).get_symmetry_dataset().pointgroup,
         )
 
         bulk_supercell = _get_bulk_supercell(defect_entry)
@@ -1428,9 +1428,7 @@ def _check_relaxed_defect_symmetry_determination(
             symprec=symprec,
             dist_tol=symprec,
         )
-        bulk_spglib_point_group_symbol = schoenflies_from_hermann(
-            symm_dataset["site_symmetry_symbols"][-1]
-        )
+        bulk_spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
 
         if bulk_spglib_point_group_symbol != unrelaxed_spglib_point_group_symbol:
             if verbose: